Parameter descriptions

Prevalance Estimates:

  • p_avg: study region prevalance
  • p_sex: prevalence within sex categories, 1=Male, 2=Female
  • p_age: prevalence within age categories: 1=[18-30), 2=[30-45), 3=[45,65), 4=[65,75), 5=[75,)
  • p_race_eth: prevalence within race/ethnicity categories: 1=White, 2=Two or more, 3=Asian or Pacific Islander, 4=American Indian or Alaskan Native or Other, 5=Hispanic, 6=African-American or Black
  • p_inc: prevalence within household income categories: 1= < $100K, 2= \(\ge\) $100K
  • p_edu: prevalence within educational attainment categories: 1= less than college degree, 2=college degree or more
  • p_zip: prevalence within 31 ZIP codes in study region
ZIP code Category
94530 1
94547 2
94564 3
94601 4
94602 5
94603 6
94605 7
94606 8
94607 9
94608 10
94609 11
94610 12
94611 13
94612 14
94618 15
94619 16
94621 17
94702 18
94703 19
94704 20
94705 21
94706 22
94707 23
94708 24
94709 25
94710 26
94801 27
94803 28
94804 29
94805 30
94806 31

Round 1

Round 1 test bias parameters:

  • se_net_r1: Sensitivty of round 1 antibody assay
  • sp_net_r1: Specificity of round 1 antibody assay

Effective Sample Size

Geweke diagnostics

Geweke results per chain
chain Num_params p p_bonf
1 61 6 0
2 61 2 0
3 61 1 0
4 61 0 0
5 61 19 2
6 61 2 0
7 61 0 0
8 61 46 2
9 61 6 0
10 61 48 12
Parameters that fail Geweke, p_bonf
chain Params
1
2
3
4
5 p_hh[2], p_hh[5]
6
7
8 p_race_eth[2], p_zip[30]
9
10 sp_net_r1, p_age[2], p_inc[2], p_race_eth[3], p_zip[3], p_zip[12], p_zip[16], p_zip[22], p_zip[23], p_zip[26], p_zip[28], sp_net_r1

Trace plots

Density plots

Autocorrelation plots

Round 2

Round 2 test bias parameters:

  • se_net_r1: Sensitivty of round 1 antibody assay
  • sp_net_r1: Specificity of round 1 antibody assay
  • se_net_r2: Sensitivty of round 2 antibody assay
  • sp_net_r2: Specificity of round 2 antibody assay
  • se_net_r1_r2: Cumulative sensitivty of round 1 + round 2 antibody assay
  • sp_net_r1_r2: Cumulative specificity of round 1 + round 2 antibody assay

Effective Sample Size

Geweke diagnostics

Geweke results per chain
chain Num_params p p_bonf
1 63 1 0
2 63 6 0
3 63 3 0
4 63 4 0
5 63 3 0
6 63 2 0
7 63 12 3
8 63 44 13
9 63 18 1
10 63 12 1
Parameters that fail Geweke, p_bonf
chain Params
1
2
3
4
5
6
7 p_zip[12], p_zip[13], p_zip[23]
8 sp_net_r1, sp_net_r1_r2, p_age[3], p_edu[2], p_hh[2], p_hh[5], p_hh[6], p_race_eth[1], p_race_eth[3], p_race_eth[5], p_white[1], p_zip[4], p_zip[31]
9 p_age[5]
10 p_zip[4]

Trace plots

Density plots

Autocorrelation plots

Round 3

Round 3 test bias parameters:

  • se_net_r1: Sensitivty of round 1 antibody assay
  • sp_net_r1: Specificity of round 1 antibody assay
  • se_net_r2: Sensitivty of round 2 antibody assay
  • sp_net_r2: Specificity of round 2 antibody assay
  • se_net_r1_r2: Cumulative sensitivty of round 1 + round 2 antibody assay
  • sp_net_r1_r2: Cumulative specificity of round 1 + round 2 antibody assay
  • se_net_r3: Sensitivty of round 3 antibody assay
  • sp_net_r3: Specificity of round 3 antibody assay
  • se_net_r1_r2_r3: Cumulative sensitivty of round 1 + round 2 + round 3 antibody assay
  • sp_net_r1_r2_r3: Cumulative specificity of round 1 + round 2 + round 3 antibody assay

Effective Sample Size

Geweke diagnostics

Geweke results per chain
chain Num_params p p_bonf
1 67 5 0
2 67 38 4
3 67 35 10
4 67 3 0
5 67 18 2
6 67 2 0
7 67 9 1
8 67 5 1
9 67 33 2
10 67 7 2
Parameters that fail Geweke, p_bonf
chain Params
1
2 p_race_eth[2], p_sex[2], p_zip[7], p_zip[12]
3 p_age[1], p_inc[2], p_zip[2], p_zip[3], p_zip[11], p_zip[13], p_zip[19], p_zip[22], p_zip[24], p_zip[28]
4
5 p_zip[7], p_zip[21]
6
7 p_zip[21]
8 p_zip[7]
9 p_zip[16], p_zip[29]
10 p_zip[8], p_zip[20]

Trace plots

Density plots

Autocorrelation plots

Round 3 spike

Effective Sample Size

Geweke diagnostics

Geweke results per chain
chain Num_params p p_bonf
1 67 46 26
2 67 11 3
3 67 15 1
4 67 35 12
5 67 14 2
6 67 33 12
7 67 31 6
8 67 9 1
9 67 13 2
10 67 15 1
Parameters that fail Geweke, p_bonf
chain Params
1 p_avg, p_age[2], p_age[3], p_age[4], p_edu[1], p_hh[1], p_hh[2], p_hh[3], p_hh[4], p_inc[1], p_inc[2], p_race_eth[1], p_race_eth[4], p_sex[1], p_sex[2], p_white[1], p_white[2], p_zip[1], p_zip[10], p_zip[12], p_zip[16], p_zip[18], p_zip[21], p_zip[28], p_zip[30], p_zip[31]
2 p_zip[1], p_zip[21], p_zip[25]
3 p_zip[28]
4 p_avg, p_age[4], p_age[5], p_hh[1], p_hh[2], p_inc[1], p_inc[2], p_race_eth[3], p_sex[1], p_sex[2], p_white[2], p_zip[13]
5 p_zip[21], p_zip[31]
6 p_age[4], p_edu[1], p_zip[5], p_zip[7], p_zip[8], p_zip[9], p_zip[11], p_zip[14], p_zip[23], p_zip[25], p_zip[29], p_zip[30]
7 p_avg, p_age[1], p_edu[1], p_inc[1], p_white[2], p_zip[10]
8 p_age[3]
9 p_zip[21], p_zip[31]
10 p_zip[27]

Trace plots

Density plots

Autocorrelation plots